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LAGOS, Nigeria (Reuters) - A military crackdown across Nigeria has hobbled Boko Haram for now, but as the army campaign intensifies it is likely to fan popular anger in the impoverished north that could ultimately make the Islamist sect's 3-year-old rebellion stronger.

The group, which wants to carve an Islamic state out of Nigeria, remains the top security threat to Africa's leading oil producer, and Western powers are worried about its growing links to more fiercely anti-Western jihadist groups in the region.

At least 2,800 people have died in fighting since the insurrection began, Human Rights Watch said on Thursday.

Nigerian soldiers and police have swept through the largely Muslim north in past weeks, raiding suspected Islamist hideouts, seizing weapons and killing or arresting scores of suspects.

Last month they intercepted a vehicle carrying the sect's spokesman and ideologue, Abu Qaqa, whom they said they killed in a shootout, although its leader Abubakar Shekau said Qaqa was captured alive.

Better policing of roads and around targets such as churches has reduced the number of deadly bomb attacks, and there has been no repeat of anything as coordinated as the strike on the north's main city of Kano in January that killed 186 people.

"A series of tactical setbacks against Boko Haram have helped to contain the militancy," said Roddy Barclay, Africa analyst at Control Risks. "But they won't bring an end to it, since they still don't address the core drivers."

Those drivers include a deep-rooted feeling of alienation among northerners, who have watched their semi-arid region stagnate while the oil-rich south enjoys relative prosperity.

They also include a burning sense of injustice among Boko Haram's members, who say their Salafist clerical movement was wrongly persecuted by the authorities in 2009. Then, Nigerian troops killed hundreds during an uprising, including sect founder Mohammed Yusuf, who died in police custody.

Jonathan's administration, seen by northerners as the most southern-Christian dominated in decades, is no less an obstacle. Boko Haram are fighting to revive an ancient Islamic caliphate in modern Nigeria, but many of their supporters might settle for a greater share of power for Muslim northerners in office.

The United States, worried that Boko Haram's fraternising with other jihaidist groups like al Qaeda could lead it to shift its focus to Western targets, has heaped pressure on Nigeria to tackle the root causes of the rebellion, with limited results.

"MORE HARMFUL THAN BOKO HARAM"

A security raid on Monday gave a taste of how Nigeria's pursuit of a military solution to the conflict could backfire.

After a bomb blast struck an army convoy passing through Maiduguri -- a dusty, bullet-ridden northeastern city on the threshold of the Sahara and the sect's official headquarters -- soldiers raided homes, shot people and burned down buildings in revenge attacks that left at least 35 dead.

"The soldiers are causing more harm than Boko Haram," said Hajiya Amina Tole, furious after seeing her house razed. "By the time they leave, our daughters will have no husbands to marry: most young men would have been killed by the military."

Yusuf Ahmed said he watched four of his friends executed in the raid and saw his family home destroyed. "If I join Boko Haram now, won't I be justified?" he asked.

Lieutenant-Colonel Sagir Musa, spokesman for joint army and police forces in the northeast, denied extrajudicial killings, and said security efforts had brought relative peace.

But analysts say they may be counterproductive longer term.

"With the government's extremely heavy-handed approach ... you have to wonder what the consequences will be in terms of acquiescence or support for Boko Haram," said John Campbell, who was U.S. ambassador to Nigeria from 2004 to 2007.

"It may have a temporary impact, but without any kind of political process, the lull won't be anything more than a lull."

Concentrated mainly in northern Nigerian, Boko Haram became active in about 2003 and is loosely modelled on the Taliban movement in Afghanistan. It considers all who do not follow its strict ideology as infidels, whether Christian or Muslim, and its followers wear bushy beards and red or black headscarves.

Nigerian authorities assumed it was finished after the 2009 crackdown. Instead, it morphed from a radical clerical movement opposed to Western culture into a fully-fledged armed rebellion.

"You're dealing with a guerrilla force that withdraws when the odds are against it but then resurfaces when the pressure eases off," said Shehu Sani, president of the Civil Rights Congress, a group calling for dialogue to resolve the crisis.

"They've been written off before, only to come back."

"LIKE AN AMOEBA"

If a military solution to the conflict is well nigh impossible, a political one is still a tall order.

Shekau's published demands include full implementation of Sharia or Islamic law in the north and a release of Boko Haram prisoners, things to which the government is unlikely to agree.

"That type of amnesty deal doesn't seem like it's even close to happening," said Jacob Zenn of the Washington-based Jamestown Foundation. "And it doesn't even seem like the religious figures are willing to implement the greater Sharia that he wants."

He suggested it might take until the next election in 2015, in which if a Muslim northerner became president, it could address some of the militants' political grievances.

Security sources believe Shekau's faction is the most hardline, but there may be others even more extreme, including smaller cells with links with global jihadists like al-Qaeda's north African wing, currently spread over the Sahara.

Boko Haram militants periodically turn up in Mali and Niger -- sometimes after being pushed out of Nigeria by the army -- then return home with more sophisticated bomb-making technology.

That underlines another of the crackdown's unintended effects, Zenn says: the militants are spreading over a wider geographical area, across the centre, east, northwest, and in neighbouring nations, facilitating their split into factions.

Despite Shekau's so far undisputed claim to lead it, Campbell says Boko Haram has become "extremely diffuse, highly uncoordinated, not at all centrally controlled."

This makes ending the insurgency by political means -- as the government claims to be trying to do via 'back channels' -- hugely complicated. And the more military pressure breaks them up into smaller groups, the more complicated it will get.

"Boko Haram is behaving like an amoeba," Sani said. "Slice it up and you just get more of them."